First it depends on what type of drives you are running as well as the speed in rpms. Here with two 250gb eide hard drives a slow down will be seen when going to copy or move either several large files or a large number of small files and folders they are in from the primary drive to the storage partition on the second. The two hard drives there run at 7,200rpm. Older drives would be seen running at 5,400rpm.
SATA hard drives run at the same 7,200rpm speed but transfer data and files on a faster bus. This allows less time to be spent trying to access files stored on that type of drive. If your drives become fragmented and disorganized from heavy use that will also see slowdowns with Windows and other programs as well as moving files around.